Just to correct original question in RLV-TD (Reusable Launch Vehicle Technology Demonstration) mission the winged body TDV (Technology Demonstration Vehicle) separated at 56 km altitude and proceeded to reach altitude of about 65 km before descent.
Yes RLV-TD configuration is unsymmetrical and unstable, former chairman of ISRO K Radhakrishnan briefly talks about that aerodynamic instability of RLV-TD, μα being 20 to 25 compared to 1 for PSLV/GSLV and 5 for LVM3 in this talk at 42 min 50 sec mark.
For control during ascent HS9 booster has RCS + SITVC system(Pitch+Yaw) for first few seconds of ascent, and later "fin tip control" as shown in following slide from presentation by M. V. Dhekane. Those four movable fins are attached to base shroud of HS9 booster. From what I have read in journal papers related to RLV-TD so far control surfaces on winged body don't play any role during ascent phase.
Official press release gives some of flight profile details. They also released a Time Vs Altitude visualization[MP4] based on telemetry from RLV-TD during flight.
I have plotted it in graph form here.
A quote from paper titled "Particle Swarm Optimization Based PI Controller Design for Actuation System of Reusable Launch Vehicle"
RLV consists of a booster stage and a fly back portion. During the ascent phase, it will be controlled by using four fin actuators. During re-entry and return flight, the altitude will be controlled by two primary control surfaces, ie, elevons and rudder.